Structure of mirMark and miRNA-target region duplex. (A) mirMark consists of two levels of classifiers, site-level and UTR-level, depending on the type of prediction desired. First, candidate target sites (CTSs) of the miRNA on the 3' UTR are found. The alignment of the CTSs and various other features concerning accessibility, conservation, and structural information are then used by the site-level classifier to find the strongest CTSs. On the other hand, the UTR-level classifier integrates the CTSs to determine if the gene is a target of the given miRNA. (B) An illustration of the site-level binding between miRNA and target regions of the 3' UTR. Information about the type of bindings that occur in the seed region is particularly predictive.